chr19-9217986-C-T

Variant names:

• chr19-9217986-C-T
• rs8101575
• NM_001005191.3:c.-14+1214G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001005191.3(OR7D4):​c.-14+1214G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0923 in 152,186 control chromosomes in the GnomAD database, including 1,260 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.092 (1260 hom., cov: 32)
• Consequence: OR7D4 NM_001005191.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.692
• Publications: 0 publications found

Genes affected

OR7D4 (HGNC:8380): (olfactory receptor family 7 subfamily D member 4) Olfactory receptors interact with odorant molecules in the nose, to initiate a neuronal response that triggers the perception of a smell. The olfactory receptor proteins are members of a large family of G-protein-coupled receptors (GPCR) arising from single coding-exon genes. Olfactory receptors share a 7-transmembrane domain structure with many neurotransmitter and hormone receptors and are responsible for the recognition and G protein-mediated transduction of odorant signals. The olfactory receptor gene family is the largest in the genome. The nomenclature assigned to the olfactory receptor genes and proteins for this organism is independent of other organisms. [provided by RefSeq, Jul 2008]

OR7E24 (HGNC:8396): (olfactory receptor family 7 subfamily E member 24) Olfactory receptors interact with odorant molecules in the nose, to initiate a neuronal response that triggers the perception of a smell. The olfactory receptor proteins are members of a large family of G-protein-coupled receptors (GPCR) arising from single coding-exon genes. Olfactory receptors share a 7-transmembrane domain structure with many neurotransmitter and hormone receptors and are responsible for the recognition and G protein-mediated transduction of odorant signals. The olfactory receptor gene family is the largest in the genome. The nomenclature assigned to the olfactory receptor genes and proteins for this organism is independent of other organisms. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.223 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001005191.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OR7D4	NM_001005191.3	MANE Select	c.-14+1214G>A		intron	N/A	NP_001005191.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OR7D4	ENST00000641669.1	MANE Select	c.-14+1214G>A		intron	N/A	ENSP00000493383.1
	OR7D4	ENST00000641244.1		c.-17+1214G>A		intron	N/A	ENSP00000493404.1

Frequencies

GnomAD3 genomes AF: 0.0922 AC: 14016 AN: 152068 Hom.: 1258 Cov.: 32

Gnomad AFR AF: 0.227

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0467

Gnomad ASJ AF: 0.0375

Gnomad EAS AF: 0.00135

Gnomad SAS AF: 0.0626

Gnomad FIN AF: 0.0305

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0433

Gnomad OTH AF: 0.0848

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0923 AC: 14045 AN: 152186 Hom.: 1260 Cov.: 32 AF XY: 0.0911 AC XY: 6777 AN XY: 74396

African (AFR) AF: 0.227 AC: 9420 AN: 41510

American (AMR) AF: 0.0466 AC: 713 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0375 AC: 130 AN: 3470

East Asian (EAS) AF: 0.00135 AC: 7 AN: 5170

South Asian (SAS) AF: 0.0630 AC: 304 AN: 4824

European-Finnish (FIN) AF: 0.0305 AC: 323 AN: 10600

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.0433 AC: 2943 AN: 68006

Other (OTH) AF: 0.0839 AC: 177 AN: 2110

Alfa AF: 0.0701 Hom.: 1355

Bravo AF: 0.101

Asia WGS AF: 0.0370 AC: 130 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.8
DANN	Benign	0.38
PhyloP100		-0.69

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs8101575; hg19: chr19-9328662;